The judges were skeptical the agency could decide whether to change the federal form, one way or the other, without any commissioners.
That would leave Kansas and Arizona without a formal decision to challenge in court.
"A political decision has been made by the political branches that they don't wish to appoint commissioners to the Elections Assistance Commission," Judge Carlos Lucero told Kansas Secretary of State Kris Kobach, who argued the case for both states. "All of a sudden the courts are asked to step into inherently political questions and make political decisions."
Kobach told the panel that preserving the status quo creates two tiers of voters in each state. "According to our Constitution, there cannot be one voter roll for state elections and another one for federal elections," he said.
In Kansas, 180 people were registered through federal forms that do not require proof of citizenship and were not permitted to vote for state offices in a primary earlier this month because they did not comply with state standards for voting.
Arizona, which has its primary Tuesday, could have hundreds or thousands of voters similarly unable to cast a ballot in state races, Kobach said.
Both states argue their requirements prevent voter fraud by thwarting voting by noncitizens. Critics of such laws view them as suppressing voter turnout, noting that there have been minimal documented cases of voter fraud and far more cases of citizens who have encountered trouble being allowed to vote under the rules. But both sides agree the potential impacts of the case could extend to other states.
Arizona voters passed their law in 2004 in response to an influx of illegal immigration and fears of voting fraud, and activists there have long complained the measure makes it harder to register members of the state's growing Hispanic population. Kansas was one of several states that passed similar laws shortly thereafter.
The appeals court panel heard the arguments on an expedited basis with the hopes of issuing a ruling before Election Day in November.
A ruling upholding the lower court's decision would likely lead to several other states demanding the federal government add their language to its voter registration forms.
The lower court judge had to order commission staff to make a decision without any seated commissioners so that Kansas and Arizona could have their day in court.
Bonnie Robin-Vergeer, who argued the case for the federal commission, contended the agency's staff had the power to make the decision and that it was the appropriate one.
Noting that Congress wants to make it easier to vote and that only citizens are permitted to cast a ballot under either system, she said: "The federal form provides a backstop, no matter what procedural hurdles a state's form may present, that there is a simple way of registering to vote."
The case has been carefully watched, with House Minority Leader Nancy Pelosi and other Democratic lawmakers joining the federal government's appeal to overturn the lower court's decision.